Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005957.1 Hibiscus syriacus cultivar Beakdansim tig00013997_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60325
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:364 original size:12 final size:12
Alignment explanation
Indices: 341--426 Score: 59
Period size: 12 Copynumber: 6.9 Consensus size: 12
331 ACTTAAAAAT
341 TAAATGAATATAA
1 TAAAT-AATATAA
354 TAAATAATATAA
1 TAAATAATATAA
366 T-AATAATAATAA
1 TAAATAAT-ATAA
* *
378 TTAGT-ATATTAA
1 TAAATAATA-TAA
* *
390 TTATTAATATAA
1 TAAATAATATAA
* *
402 TACATAATTAAAA
1 TAAATAA-TATAA
415 TATAATAATATA
1 TA-AATAATATA
427 GTAATTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 7 0.12
12 29 0.49
13 19 0.32
14 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (12 bp):
TAAATAATATAA
Found at i:371 original size:18 final size:18
Alignment explanation
Indices: 350--424 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
340 TTAAATGAAT
*
350 ATAATAAATAATATAATA
1 ATAATTAATAATATAATA
368 ATAA-TAATAAT-TAGTATA
1 ATAATTAATAATATA--ATA
* *
386 TTAATTATTAATATAATA
1 ATAATTAATAATATAATA
404 CATAATTAA-AATATAATA
1 -ATAATTAATAATATAATA
422 ATA
1 ATA
425 TAGTAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 2 0.04
17 9 0.19
18 22 0.47
19 12 0.26
20 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAATTAATAATATAATA
Found at i:424 original size:21 final size:22
Alignment explanation
Indices: 398--438 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
388 AATTATTAAT
398 ATAATACA-TAATTAAAATATA
1 ATAATACAGTAATTAAAATATA
*
419 ATAATATAGTAATTAAAATA
1 ATAATACAGTAATTAAAATA
439 GATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAATACAGTAATTAAAATATA
Found at i:3089 original size:20 final size:20
Alignment explanation
Indices: 3040--3109 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3030 TATTGTTCAT
* * * *
3040 TACTGTTCACATAGTATTGG
1 TACTATTCATATAGTATCGA
3060 TACTATTCATATAGTATCGA
1 TACTATTCATATAGTATCGA
*
3080 TACTATTCATACAGTA-C-A
1 TACTATTCATATAGTATCGA
3098 GTACTATTCATA
1 -TACTATTCATA
3110 AAAACATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
18 1 0.02
19 12 0.27
20 31 0.70
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
TACTATTCATATAGTATCGA
Found at i:10842 original size:23 final size:22
Alignment explanation
Indices: 10790--10842 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
10780 AATTTATATA
**
10790 AAATTTTAAAAAAGAAAATTAT
1 AAATTTTAAAAAAGAAAAACAT
* *
10812 ATATTTTTAAAAAATAAATAACAT
1 A-AATTTTAAAAAAGAAA-AACAT
10836 AAATTTT
1 AAATTTT
10843 GAAATAACCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTTTAAAAAAGAAAAACAT
Found at i:13443 original size:18 final size:19
Alignment explanation
Indices: 13406--13444 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13396 CTTAAACTTT
* *
13406 TTTATTATTTTATTATAAA
1 TTTAATATTTTATAATAAA
13425 TTTAATATTTT-TAATAAA
1 TTTAATATTTTATAATAAA
13443 TT
1 TT
13445 ATCAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAATATTTTATAATAAA
Found at i:15755 original size:19 final size:19
Alignment explanation
Indices: 15713--15754 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15703 TTTAAACTAT
*
15713 AATAAAATTATAAATAAAA
1 AATATAATTATAAATAAAA
15732 AATATAATTAT-AAT-AAA
1 AATATAATTATAAATAAAA
15749 AATATA
1 AATATA
15755 TTTTATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAATTATAAATAAAA
Found at i:16530 original size:21 final size:21
Alignment explanation
Indices: 16506--16549 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16496 ATCATCGTCC
*
16506 ATCGAGTACTGTCACAAT-AAT
1 ATCGAGAACTGTCA-AATCAAT
*
16527 ATCGTGAACTGTCAAATCAAT
1 ATCGAGAACTGTCAAATCAAT
16548 AT
1 AT
16550 TGTAGATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
ATCGAGAACTGTCAAATCAAT
Found at i:18892 original size:31 final size:31
Alignment explanation
Indices: 18857--18921 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
18847 AAGTCGGGTA
18857 TCGGGTCAAGTTGAA-ATCAGATCAGTTGGAT
1 TCGGGTCAAGTT-AATATCAGATCAGTTGGAT
** * *
18888 TCGGGTCTGGTTAATATCGGATCGGTTGGAT
1 TCGGGTCAAGTTAATATCAGATCAGTTGGAT
18919 TCG
1 TCG
18922 AGTCGAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (31 bp):
TCGGGTCAAGTTAATATCAGATCAGTTGGAT
Found at i:18998 original size:20 final size:20
Alignment explanation
Indices: 18973--19011 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18963 TTTCAATTCA
*
18973 GGTCAACCTTTAGATTTTTG
1 GGTCAACATTTAGATTTTTG
18993 GGTCAACATTTAGATTTTT
1 GGTCAACATTTAGATTTTT
19012 AAGTTAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (20 bp):
GGTCAACATTTAGATTTTTG
Found at i:27276 original size:23 final size:23
Alignment explanation
Indices: 27250--27364 Score: 131
Period size: 23 Copynumber: 5.0 Consensus size: 23
27240 CACCACAGCT
* *
27250 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
* ** *
27273 CGTAGAATTACAATGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
*
27296 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
* * *
27319 CGTAGAATTACAACGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
*
27342 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
27365 TATAATAATG
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:27322 original size:46 final size:46
Alignment explanation
Indices: 27250--27364 Score: 203
Period size: 46 Copynumber: 2.5 Consensus size: 46
27240 CACCACAGCT
* * *
27250 CGTATAATTGCACCGAAGTGCCACGTAGAATTACAATGGAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCACGTAGAATTACAACGGAGTGCCG
27296 CGTAGAATTGCACCGTAGTGCCACGTAGAATTACAACGGAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCACGTAGAATTACAACGGAGTGCCG
27342 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
27365 TATAATAATG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (46 bp):
CGTAGAATTGCACCGTAGTGCCACGTAGAATTACAACGGAGTGCCG
Found at i:32024 original size:31 final size:31
Alignment explanation
Indices: 31927--32082 Score: 201
Period size: 31 Copynumber: 5.1 Consensus size: 31
31917 GAAGGACCTA
* * *
31927 TCCAGAGGTCACAAAGA-CCCCGGT-AACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
*
31956 TCCAGAGGTCATAAAGATCCTCGGT-AACTT
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
31986 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
32017 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
* *** * *
32048 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
32079 TCCA
1 TCCA
32083 TATGTCTCGA
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.14
30 35 0.30
31 64 0.56
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (31 bp):
TCCAGAGGTCATAAAGATCCTCGGTAAACTG
Found at i:32083 original size:31 final size:31
Alignment explanation
Indices: 31981--32107 Score: 103
Period size: 31 Copynumber: 4.1 Consensus size: 31
31971 GATCCTCGGT
* * ** * *
31981 AACTTTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* ** * *
32012 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
*
32043 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* * *
32074 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCACGAAGA-ACCTAGGTA
32105 AAC
1 AAC
32108 CCTCGACTCT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 1 0.01
31 84 0.99
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCACGAAGAACCTAGGTA
Found at i:32610 original size:2 final size:2
Alignment explanation
Indices: 32603--32627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32593 ATACAATTCC
32603 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32628 CTAACTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32832 original size:19 final size:19
Alignment explanation
Indices: 32808--32859 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
32798 TGTAATACAA
32808 CTAAACATATTCATGTAAT
1 CTAAACATATTCATGTAAT
32827 CTAAACATATTCATGTAAT
1 CTAAACATATTCATGTAAT
*
32846 CTAAACATAATCAT
1 CTAAACATATTCAT
32860 ACAATCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (19 bp):
CTAAACATATTCATGTAAT
Found at i:32865 original size:19 final size:19
Alignment explanation
Indices: 32802--32865 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
32792 CTAACATGTA
32802 ATACAA-CTAAACATATTC
1 ATACAATCTAAACATATTC
**
32820 ATGTAATCTAAACATATTC
1 ATACAATCTAAACATATTC
** *
32839 ATGTAATCTAAACATAATC
1 ATACAATCTAAACATATTC
32858 ATACAATC
1 ATACAATC
32866 ATATATTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 4 0.10
19 36 0.90
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (19 bp):
ATACAATCTAAACATATTC
Found at i:33233 original size:21 final size:21
Alignment explanation
Indices: 33203--33247 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
33193 ATTCTGTCGT
*
33203 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
33224 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
33245 TTG
1 TTG
33248 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:36539 original size:30 final size:31
Alignment explanation
Indices: 36483--36613 Score: 196
Period size: 31 Copynumber: 4.3 Consensus size: 31
36473 GAAGGACCTA
* * *
36483 TCCAGAGGTCACAAAGA-CCCCGGT-AACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
36512 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
*
36542 TCAAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
36573 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
*
36604 TCCATAGGTC
1 TCCAGAGGTC
36614 CCGAAGAACC
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.17
30 34 0.36
31 44 0.47
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (31 bp):
TCCAGAGGTCATAAAGATCCTCGGTAAACTG
Found at i:36585 original size:61 final size:60
Alignment explanation
Indices: 36486--36605 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 60
36476 GGACCTATCC
36486 AGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AACTGTCA
1 AGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAAACTGTCA
* * *
36545 AGAGGTCATAAAGATCCTCGGTAAACTGTCCAGAGGTCATAAAGATCCTCGGTAAACTGTC
1 AGAGGTCACAAAGA-CCCCGGT-AACTATCCAGAGGTCATAAAGATCCTCGGTAAACTGTC
36606 CATAGGTCCC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 13 0.24
60 6 0.11
61 29 0.53
62 7 0.13
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (60 bp):
AGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAAACTGTCA
Found at i:36630 original size:31 final size:31
Alignment explanation
Indices: 36537--36663 Score: 94
Period size: 31 Copynumber: 4.1 Consensus size: 31
36527 GATCCTCGGT
* * ** * *
36537 AACTGTCAAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* ** * *
36568 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
*
36599 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* * * *
36630 AACCGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCACGAAGA-ACCTAGGTA
36661 AAC
1 AAC
36664 CCTCGACTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 1 0.01
31 83 0.99
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCACGAAGAACCTAGGTA
Found at i:36638 original size:62 final size:61
Alignment explanation
Indices: 36486--36638 Score: 175
Period size: 62 Copynumber: 2.5 Consensus size: 61
36476 GGACCTATCC
** **
36486 AGAGGTCACAAAG-ACCCCGGT-AACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCA
1 AGAGGTCACAAAGAACCTAGGTAAACCGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCA
* * * * *
36545 AGAGGTCATAAAGATCCTCGGTAAACTGTCCAGAGGTCATAAAGATCCTCGGTAAACTGTCC
1 AGAGGTCACAAAGAACCTAGGTAAACCGTCCAGAGGTCATAAAGATCCTCGGT-AACTGTCA
* * *
36607 ATAGGTCCCGAAGAACCTAGGTAAACCGTCCA
1 AGAGGTCACAAAGAACCTAGGTAAACCGTCCA
36639 TATGTCTCGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 12 0.15
60 6 0.08
61 29 0.37
62 32 0.41
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (61 bp):
AGAGGTCACAAAGAACCTAGGTAAACCGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCA
Found at i:37408 original size:19 final size:19
Alignment explanation
Indices: 37364--37408 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
37354 CTAACATGTA
*
37364 ATACAA-CTAAACATATTC
1 ATACAATCTAAACATAATC
**
37382 ATGTAATCTAAACATAATC
1 ATACAATCTAAACATAATC
37401 ATACAATC
1 ATACAATC
37409 ATATATTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (19 bp):
ATACAATCTAAACATAATC
Found at i:37777 original size:21 final size:21
Alignment explanation
Indices: 37747--37791 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37737 ATTCTGTCGT
* *
37747 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37768 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
37789 TTG
1 TTG
37792 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39881 original size:23 final size:23
Alignment explanation
Indices: 39855--39907 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
39845 ATTACAATGA
*
39855 AGTGCCACGTAGAATTGCACCAG-
1 AGTGCCACGCAGAATTGCACC-GT
*
39878 AGTGCCGCGCAGAATTGCACCGT
1 AGTGCCACGCAGAATTGCACCGT
39901 AGTGCCA
1 AGTGCCA
39908 TATAATAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.17
Consensus pattern (23 bp):
AGTGCCACGCAGAATTGCACCGT
Found at i:41459 original size:24 final size:21
Alignment explanation
Indices: 41428--41475 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
41418 CAATATTCAT
41428 TTCTTCCTTTAGGGGGGAATCGG
1 TTCTTCC--TAGGGGGGAATCGG
* *
41451 TTCTCTCCTATGGGGGTATCGG
1 TTCT-TCCTAGGGGGGAATCGG
41473 TTC
1 TTC
41476 CCCCATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 15 0.68
23 4 0.18
24 3 0.14
ACGTcount: A:0.10, C:0.21, G:0.31, T:0.38
Consensus pattern (21 bp):
TTCTTCCTAGGGGGGAATCGG
Found at i:41530 original size:21 final size:21
Alignment explanation
Indices: 41506--41548 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41496 TCTGGTTTGT
* * *
41506 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41527 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41548 T
1 T
41549 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42696 original size:15 final size:15
Alignment explanation
Indices: 42685--42741 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
42675 ATTTAAAAAG
42685 AAAAATAATAAAATA
1 AAAAATAATAAAATA
*
42700 AATAATAAT-AAATA
1 AAAAATAATAAAATA
**
42714 AAAAA-AGGGAAAATA
1 AAAAATA-ATAAAATA
42729 ATAAAATAATAAA
1 A-AAAATAATAAA
42742 TAATAGTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
13 1 0.03
14 9 0.28
15 14 0.44
16 7 0.22
17 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAAATAATAAAATA
Found at i:42698 original size:35 final size:37
Alignment explanation
Indices: 42654--42746 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
42644 TTGAAAAGAT
* **
42654 ATAATAAAATAAATAATTAT-AATTTAAAAA-GAAAA
1 ATAATAAAATAAATAATAATAAATAAAAAAAGGAAAA
*
42689 ATAATAAAATAAATAATAATAAATAAAAAAAGGGAAA
1 ATAATAAAATAAATAATAATAAATAAAAAAAGGAAAA
42726 ATAATAAAAT-AATAAATAATA
1 ATAATAAAATAAAT-AATAATA
42747 GTAGTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
35 19 0.37
36 11 0.22
37 21 0.41
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAATAAAATAAATAATAATAAATAAAAAAAGGAAAA
Found at i:42813 original size:18 final size:18
Alignment explanation
Indices: 42790--42832 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42780 GTTTTAAAAA
42790 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
*
42808 AAATAAAGGAAAATAATT
1 AAATAAAAGAAAATAATT
42826 AAATAAA
1 AAATAAA
42833 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:50263 original size:27 final size:27
Alignment explanation
Indices: 50231--50282 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
50221 TCAAGGAAGT
*
50231 GGTGGAACACGAGGAAGTGTTGGAAAC
1 GGTGGAACACGAGGAAGTGCTGGAAAC
*
50258 GGTGGAACACGAGGTAGTGCTGGAA
1 GGTGGAACACGAGGAAGTGCTGGAA
50283 CACGCGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.42, T:0.15
Consensus pattern (27 bp):
GGTGGAACACGAGGAAGTGCTGGAAAC
Found at i:51287 original size:16 final size:16
Alignment explanation
Indices: 51266--51300 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
51256 TCTCTGGTTG
51266 TATCTATGTAATTTCT
1 TATCTATGTAATTTCT
51282 TATCTATGTAATTTCT
1 TATCTATGTAATTTCT
51298 TAT
1 TAT
51301 GTTTAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (16 bp):
TATCTATGTAATTTCT
Found at i:54518 original size:22 final size:20
Alignment explanation
Indices: 54484--54523 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54474 ATTTTTTTAT
*
54484 TAATATATGTAAATATAAAG
1 TAATATATGTAAAGATAAAG
54504 TAATATATGTTTAAAGATAA
1 TAATATATG--TAAAGATAA
54524 TTTTCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
TAATATATGTAAAGATAAAG
Done.